Evidence map›Paper›PMID 37089777›Full record

ArticleOpen forum infectious diseases2023

Surveillance of Severe Acute Respiratory Syndrome Coronavirus 2 and Variants Using Digital Droplet Polymerase Chain Reaction at a Large University and Healthcare System in California.

Chrysovalantis Stafylis, Olivier Pernet, Cassidy Hernandez-Tamayo, Andrea Kovacs, Jane Emerson, Pamela M Ward, Sarah Van Orman, Frank Gilliland, David Conti, Maia Weisenhaus and 21 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Open forum infectious diseases, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.1field-weighted citation impact, top 63% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 1 citations in OpenAlex.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

31 authors at 2 institutions in 1 country.

Chrysovalantis StafylisDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.ORCID https://orcid.org/0000-0002-1486-1130
Olivier PernetMaternal, Child and Adolescent Center for Infectious Diseases, University of Southern California, Los Angeles, California, USA.
Cassidy Hernandez-TamayoDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
Andrea KovacsMaternal, Child and Adolescent Center for Infectious Diseases, University of Southern California, Los Angeles, California, USA.
Jane EmersonDepartment of Pathology and Laboratory Medicine in Keck, University of Southern California, Los Angeles, California, USA.
Pamela M WardDepartment of Pathology and Laboratory Medicine in Keck, University of Southern California, Los Angeles, California, USA.
Sarah Van OrmanDepartment of Family Medicine, University of Southern California, Los Angeles, California, USA.
Frank GillilandDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
David ContiDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
Maia WeisenhausMaternal, Child and Adolescent Center for Infectious Diseases, University of Southern California, Los Angeles, California, USA.
Angie Ghanem-UzquedaDepartment of Family Medicine, University of Southern California, Los Angeles, California, USA.
Daniel YepezDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
Sofia StellarDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
Aditya P TadankiDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
Jillian MaxDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
Honour FottrellDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
Ethan OngDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
Sabrina NavarroDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
Kaelyn MosesDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
Michael AkaolisaDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
Bijan HosseiniDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
Shaleen SunesaraDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
Yuzhu WangDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
Earl StrumKeck Hosptial of USC, Employee Health, Los Angeles, California, USA.
Yolee CasagrandeKeck Hosptial of USC, Employee Health, Los Angeles, California, USA.
Nathalie ArenasKeck Hosptial of USC, Employee Health, Los Angeles, California, USA.
Christopher WilliamsDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
Paul ThomasDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.ORCID https://orcid.org/0000-0002-9074-3507
Tara ChuDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
Howard HuDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
Jeffrey D KlausnerDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA.
University of Southern California · USKeck Hospital of USC · US

Funding

Southern California Clinical and Translational Science InstituteUL1TR001855 · NCATS · UNIVERSITY OF SOUTHERN CALIFORNIA · PI Thomas A Buchanan, Michele D. Kipke · 2016 to 2026
$81.3M
Southern California Clinical and Translational Science InstituteUL1TR000130 · NCATS · UNIVERSITY OF SOUTHERN CALIFORNIA · PI BUCHANAN, THOMAS A · 2012 to 2015
$36.0M
Long-term Effects of IDU, HIV, HCV and the Impact of HCV Cure on Immune Activation and Liver Fibrosis in Aging WomenR01DA044111 · NIDA · UNIVERSITY OF SOUTHERN CALIFORNIA · PI KOVACS, ANDREA A.Z., TIEN, PHYLLIS C · 2017 to 2021
$3.5M
NCATS NIH HHS UL1 TR000130NCATS NIH HHS UL1 TR001855NIDA NIH HHS R01 DA044111
6 · The paper itself

Abstract

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with different infectivity, transmission potential, and morbidity change the characteristics of local epidemics and affect vaccine effectiveness. As part of the University of Southern California COVID-19 Pandemic Research Center's efforts to understand, control, and inform local community on coronavirus disease 2019 (COVID-19), we implemented a SARS-CoV-2 surveillance program among students, employees, and USC Keck Medical Center patients. We present the epidemiology and distribution of SARS-CoV-2 and its variants among the population. Methods: We used digital droplet reverse-transcriptase polymerase chain reaction (PCR) to analyze in real-time remnant SARS-CoV-2 PCR-positive saliva specimens stored at the USC Keck Medicine laboratory between September 2020 and April 2022. Samples were tested for the original strain (A20) and 9 SARS-CoV-2 variants: α(B.1.1.7, Q.1-Q.8), β(B.1.351, B.1.351.2, B.1.351.3), γ(P.1, P.1.1, P.1.2), δ(B.1.617.2), δ+(or δ417N), ε(B.1.427 and B.1.429), η(B.1.525), λ(C.37) and ο(B.1.1.529, ΒΑ.1, BA.2). We reviewed deidentified health information from positive cases including demographics, history of COVID-19 (eg, symptoms, hospitalizations, and repeat infections), and COVID-19 vaccination status. Results: We reviewed 1169 cases and determined the variant type of 482 specimens: 77 specimens were original strain, 119 "Delta", 165 "Omicron". The original strain was detected during the third and fourth quarters of 2020. The Delta variant appeared during the second quarter of 2021, whereas Omicron appeared in the fourth quarter of 2021. Conclusions: Prospectively tracking SARS-CoV-2 variants in a university population and a hospital system, utilizing a low-cost, high-throughput PCR assay, was feasible. Local variant monitoring remains important to inform prevention and control efforts among university and clinical settings.

Indexed as

COVID-19SARS-CoV-2surveillanceuniversityvariants

Identifiers

PMID37089777
PMCPMC10117372
OpenAlexW4327723524

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.